| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Human normal pancreas | University of California, Davis Comprehensive Cancer Center | N/A |
| Critical commercial assays | ||
| Qiagen DNEasy Blood and Tissue Kit | Qiagen | Cat#69504 |
| Accel-NGS Methyl-Seq DNA Library Kit | Swift Biosciences | Cat#30096 |
| Deposited data | ||
| WGBS raw data and processed bedgraph files | This paper | GEO: GSE243528 |
| Custom code | This paper | https://github.com/swang52/pdac_wgbs.git |
| Mouse reference genome NCBI37/mm9 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/grc/mouse |
| Human reference genome GRCh38/hg38 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/grc/human |
| mT and mM organoid RNA-seq data | Oni et al.34 | GEO: GSE142467 |
| mT and mM H3K4me1 and H3K27ac ChIP-seq data | Roe et al.33 | GEO: GSE99311 |
| GATA6 ChIP in PATU8988S cells | Kloesch et al.44 | GEO: GSE47535 |
| TET TKO WGBS, ATAC-seq, RNA-seq, and ChIP-seq data | Li et al.45 | GEO: GSE146486 |
| HNF4A ChIP in PDAC cells | Camolotto et al.52 | GEO: GSE138452 |
| Biological samples | ||
| Mouse: mN5 Normal pancreatic organoid | Tuveson Laboratory, Boj et al.20 | NA |
| Mouse: mN11 Normal pancreatic organoid | Tuveson Laboratory, Boj et al.20 | NA |
| Mouse: mP1 PanIN organoid | Tuveson Laboratory, Boj et al.20 | NA |
| Mouse: mP2 PanIN organoid | Tuveson Laboratory, Boj et al.20 | NA |
| Mouse: mT3 Tumor organoid | Tuveson Laboratory, Boj et al.20 | NA |
| Mouse: mT6 Tumor organoid | Tuveson Laboratory, Boj et al.20 | NA |
| Mouse: mT19 Tumor organoid | Tuveson Laboratory, Roe et al.33 | NA |
| Mouse: mT23 Tumor organoid | Tuveson Laboratory, Roe et al.33 | NA |
| Mouse: mM1 Metastatic organoid (liver, paired tumor is mT3) | Tuveson Laboratory, Boj et al.20 | NA |
| Mouse: mM3P Metastatic organoid (peritoneum, paired tumor is mT6) | Tuveson Laboratory, Boj et al.20 | NA |
| Mouse: mM6 Metastatic organoid (peritoneum, paired tumor is mT19) | Tuveson Laboratory, Roe et al.33 | NA |
| Mouse: mM10 Metastatic organoid (peritoneum, paired tumor is mT23) | Tuveson Laboratory, Roe et al.33 | NA |
| Human: hN1 Normal pancreatic organoid (female, 59 years old) | This paper | NA |
| Human: hN4 Normal pancreatic organoid (female, unknown age) | Tuveson Laboratory, Boj et al.20 | NA |
| Human: hN9 Normal pancreatic organoid (female, unknown age) | Tuveson Laboratory, Boj et al.20 | NA |
| Human: hN18 Normal pancreatic organoid (male, 69 years old) | This paper | NA |
| Human: SNU-3898-TO Tumor organoid (female, 61 years old) | Korean Cell Line Bank | NA |
| Human: SNU-3912-TO Tumor organoid (female, 58 years old) | Korean Cell Line Bank | NA |
| Human: SNU-3926-TO Tumor organoid (female, 52 years old) | Korean Cell Line Bank | NA |
| Human: SNU-3947-TO Tumor organoid (female, 64 years old) | Lee et al.53 | NA |
| Human: SNU-3997-TO Tumor organoid (male, 54 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4158-TO Tumor organoid (female, 54 years old) | Lee et al.53 | NA |
| Human: SNU-4192-TO Tumor organoid (female, 56 years old) | Lee et al.53 | NA |
| Human: SNU-4206-TO Tumor organoid (female, 81 years old) | Lee et al.53 | NA |
| Human: SNU-4208-TO Tumor organoid (male, 45 years old) | Lee et al.53 | NA |
| Human: SNU-4242-TO Tumor organoid (male, 74 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4243-TO Tumor organoid (male, 63 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4305-TO Tumor organoid (female, 65 years old) | Lee et al.53 | NA |
| Human: SNU-4340-TO Tumor organoid (male, 66 years old) | Lee et al.53 | NA |
| Human: SNU-4354-TO Tumor organoid (female, 64 years old) | Lee et al.53 | NA |
| Human: SNU-4365-TO Tumor organoid (female, 55 years old) | Lee et al.53 | NA |
| Human: SNU-4378-TO Tumor organoid (female, 69 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4425-TO Tumor organoid (female, 60 years old) | Lee et al.53 | NA |
| Human: SNU-4457-TO Tumor organoid (female, 58 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4461-TO Tumor organoid (female, 67 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4482-TO Tumor organoid (female, 65 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4525-TO Tumor organoid (male, 56 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4557-TO Tumor organoid (female, 63 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4779-TO Tumor organoid (female, 62 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4837-TO Tumor organoid (male, 67 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4863-TO Tumor organoid (female, 69 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4871-TO Tumor organoid (female, 58 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4874-TO Tumor organoid (female, 54 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4893-TO Tumor organoid (male, 69 years old) | Korean Cell Line Bank | NA |
| Human: SNU-4894-TO Tumor organoid (male, 61 years old) | Korean Cell Line Bank | NA |
| Human: SNU-5177-TO Tumor organoid (female, 57 years old) | Korean Cell Line Bank | NA |
| Human: SNU-5345-TO Tumor organoid (male, 54 years old) | Korean Cell Line Bank | NA |
| Software and algorithms | ||
| CpG_Me | Laufer et al.54 | https://github.com/ben-laufer/CpG_Me |
| Trim Galore | Babraham Bioinformatics | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| Cutadapt | Martin55 | https://cutadapt.readthedocs.io/en/stable/ |
| FastQ Screen | Wingett et al.56 | https://www.bioinfromatics.babraham.ac.uk/projects/fastq_screen/ |
| Bismark | Krueger and Andrews57 | https://www.bioinformatics.babraham.ac.uk/projects/Bismark |
| Bowtie 2 | Langmead and Salzberg58 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| SAMtools | Li et al.59 | https://www.htslib.org |
| Picard | Broad Institute | https://broadinstitute.github.io/picard/ |
| MultiQC | Ewels et al.60 | https://multiqc.info |
| R | https://www.r-project.org/ | |
| DMRichR | Laufer et al.54 | https://github.com/ben-laufer/DMRichR |
| Dmrseq | Korthauer et al.61 | https://bioconductor.org/packages/release/bioc/html/dmrseq.html |
| Bsseq | Hansen et al.62 | https://bioconductor.org/packages/release/bioc/html/bsseq.html |
| ComplexHeatmap | Gu et al.63 | https://jokergood.github.io/ComplexHeatmap-reference/book/ |
| enrichR | Chen et al.64 | https://cran.r-project.org/web/packages/enrichR/index.html |
| HOMER | Heinz et al.65 | htttps://homer.ucsd.edu/homer |
| LOLA | Sheffield and Bock66 | https://bioconductor.org/packages/release/bioc/html/LOLA.html |
| liftOver | UCSC | https://genome.ucsc.edu/cgi-bin/hgLiftOver |
| Boruta | Kursa and Rudnicki67 | https://cran.r-project.org/web/packages/Boruta/index.html |
| sigFeature | Das et al.68 | https://www.bioconductor.org/packages/release/bioc/html/sigFeature.html |
| DESeq2 | Love et al.35 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| ggplot2 | Wickham69 | https://cran.r-project.org/web/packages/ggplot2/index.html |
| Graphpad Prism | GraphPad Software | https://www.graphpad.com/features |
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